Chrome window keeps disappearing

Something that you might want to check is the amount of chrome.exe processes out. AFAIK it creates one for every tab and one main process. Check if any are missing.

I've had this happen once but it was because of a program to enhance my second screen, which I don't assume you use.

No, I don't use a separate screen. Also, just checking now, I only have 4 chrome tabs open but my taskmanager has 16 chrome.exe*32 processes running.